An interesting observation --
RasMol uses a "DSSP" method of calculating double bonds without actually
doing the DSSP calculation. What that does is -- it seems to me --
improperly assign hydrogen bonds. If you read the DSSP paper carefully, you
see that although the same calculation is presented there for hydrogen bond
detection as used in RasMol (well, ALMOST the same...) the intent is to
define sheet and helix structure, not to correctly identify all hydrogen
bonds. Kabsch and Sander were purposely and explicitly generous in their
assignments.
It seems to me a smarter idea would be to use the DSSP algorithm to select
only the defining hydrogen bonds that are used to identify helix, turn, and
bridge positions.
Also, for the record, RasMol does not identify inter-chain hydrogen bonds,
which is also a bug, as far as I can tell -- or at least a misreading of the
DSSP paper.
Here's a comparison:
Rasmol: http://stolaf.edu/people/hansonr/jmol/1gua-rasmol.png
Jmol (with DSSP): http://stolaf.edu/people/hansonr/jmol/1gua-jmol.png
The bonds in the Jmol version are colored by type (antiparallel white and
parallel cyan)
Comments?
Bob
On Fri, Oct 1, 2010 at 1:21 PM, Thomas Stout <thomasjst...@gmail.com> wrote:
>
>
> a big "YES" from here too!
>
> That would be great
> -Tom
>
>
>
> On Thu, Sep 30, 2010 at 8:30 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Jmol users interested in protein visualization:
>>
>> Is there any interest in having Jmol be able to calculate (verifiably
>> proper) DSSP secondary structure for proteins -- alpha helices, 3/10
>> helices, pi-helices, turns, antiparallel and parallel ladders, etc.?
>>
>> Thanks.
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
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>>
>>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
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>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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